It should be mentioned that nobody has ever been banned/bricked/etc for using a flashcart on the 3DS in nearly 2 years, which is more or less the same situation. All Nintendo does is block the flashcards in updates.
That's true, but the flashcarts are DS-mode. I doubt we'll start seeing console bans until Wii U or 3DS mode is hacked. It certainly is a possibility though.
I do wonder how 3DS flashcarts will work. Since for example MK7 requires the 1.1 update to play online, I wonder if people will simply be unable to play online in MK7 with flashcarts, or if they'll have to patch the ROM manually with the update (which isn't likely to be immediately possible when flashcarts or another way to play roms is released)
If, when it gets hacked eventually, you could simply install the games on the SD card like any eShop game, updates should work just fine and so would your statistics in the friend list, but that might be easier to detect/block for Nintendo than a flashcart.
But that's getting kind of off topic, so back on topic:
No one can say if Nintendo will start banning people from online, but since they seem to be focusing more on piracy prevention now it might very well happen.
I certainly hope not, because there is no way I won't soft/hardmod my Wii U once it's fully hacked.
I'm most likely going to hack Wii Mode soon as well, and use USB loading on it so I can pack away my Wii (either by using SNEEK+DI or waiting for cIOSes to be updated). I don't think they'll ban people for installing Wii Mode homebrew but it certainly is a possibility.